 ../
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AAinfo.java
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524
(12 years ago)
by duarte:
Fixed reading od PDB files. We hope now to be catching all possible errors present in original PDB files, plus we read correctly CASP TS files:
- now reading (and requiring) TARGET record for CASP TS files
- now we always have (and require) a sequence (possibly with ? or X) for all cases: PdbfilePdb, CaspRRFileRIGraph, FileRIGraph.
- in PDB files we throw format exceptions for: insertion codes, residue numbers <=0, non-ascending order of residue numbers in atom lines, when residues of SEQRES seq and ATOM seq don't match. In addition we warn when starting residue in ATOM lines is >100
- we allow PDB files without a HEADER, i.e. only ATOM lines
New fields in Pdb for CAPS identifiers: passed all the way down to RIGraphs in getGraph()
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AIGEdge.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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AIGNode.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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AIGraph.java
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659
(12 years ago)
by stehr:
Also adding caspParents member to graph classes, value will be kept from Pdb if present; adding method to GraphAverager to retrieve the most frequently used parents specified in the templates
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Alignment.java
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641
(12 years ago)
by stehr:
added option to GraphAverager and averageGraph to create dummy sequence with length of alignment to view the overlaid graphs without mapping to a target sequence
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AlignmentConstructionError.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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Box.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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CaspRRFileData.java
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644
(12 years ago)
by duarte:
New feature: averageGraph now also writes out the CASP RR file (if -c specified) for the average graph at Cb 8.
Made a bit prettier the CASP RR output: now contacts sorted and weights with only 2 decimal figures.
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CaspRRFileRIGraph.java
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543
(12 years ago)
by duarte:
Now forcing i<j in CASP RR files (as specified by the CASP RR format)
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CatalSiteSet.java
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514
(13 years ago)
by filippis:
Latest scop and csa versions updated.
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CatalyticSite.java
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503
(13 years ago)
by filippis:
createGraphDb:
-scop_graph table added
-!!!!residue serial fields (num, i_num, j_num) are changed to unsigned
!!!!ProtStructGraph:
-interSSE variable added
-getResidueSerial abstract method added
-restrictContactsBetweenSs method added
!!!!AIGraph:
-getResidueSerial method added
RIGraph:
-!!!!getResidueSerial method added
-scop graphs are written to db correctly
-interSSE variable taken into account for CR db field
DbRIgraph:
-changes made so to be able to read from db using a scop id
-interSSE and minSeqSep are set now in get_db_graph_info()
-!!!!FIXED BUG:fullLength in read_graph_from_db is not set to the size of the serials2nodes TreeMap instead of the maximum serial in serials2nodes. It was giving wrong result for scop graphs.
testDbRIGraph added:
It reads one graph from a source db based either
-on pdbcode, chaincode and graph properties or
-on scop id and graph properties or
-on a graph id
and it writes the graph to a destination db.
Pdb:
-unused scop regions are now removed in restrictToScopDomain
-unused residues are also removed from resser2pdbresser, pdbresser2resser, resser2allrsa, resser2scrsa, resser2consurfhsspscore, resser2consurfhsspcolor, catalSiteSet
-!!!!sequence is reset to scop sequence and fullLength to the length of the scop sequence
CatalSiteSet:
- removeCatalSiteRes(int resser) method added
CatalyticSite:
-remRes(int resser) method added
Scop:
-remove(ScopRegion e) method added
genDbGraph:Comments only added to demonstrate new functionality.
-comment added to show how to use restrictContactsBetweenSs
-comment added to show how to use restrictToScopDomain
-runDssp now is always run and not only when mode != "GRAPH". This has been changed since now the contact range might depend on the ss assignment (restrictContactsBetweenSs) and we want to ensure consistent results
-runNaccess moved to the bottom so it is always run last. In this way if restrictToScopDomain is used, we don't have to run naccess twice.
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CiffileFormatError.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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CiffilePdb.java
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639
(12 years ago)
by duarte:
Implemented parsing of PsiPred secondary structure prediction files in SecondaryStructure class.
New member in SecondaryStructure: sequence. Constructor must pass the sequence now, changed all references.
New method in Alignment to print a "graphical" matching of secondary structures.
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ConformationsNotSameSizeError.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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ContactType.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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DbRIGraph.java
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639
(12 years ago)
by duarte:
Implemented parsing of PsiPred secondary structure prediction files in SecondaryStructure class.
New member in SecondaryStructure: sequence. Constructor must pass the sequence now, changed all references.
New method in Alignment to print a "graphical" matching of secondary structures.
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EC.java
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502
(13 years ago)
by stehr:
EC, CatalSiteSet: added typing to some iterators to avoid eclipse warning
Interval: added typing to Comparator to avoid eclipse warning
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ECRegion.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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FastaFileFormatError.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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FileFormatError.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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FileRIGraph.java
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551
(12 years ago)
by duarte:
Fixed bug: now reading/writing #MODEL field in contact map files
In Pdb writeAtomLines now prints a nicer header with source info depending on source: file or db
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FileTypeGuesser.java
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550
(12 years ago)
by stehr:
changed header of contact map file from #AGLAPPE... to #CMVIEW...; when reading, both are accepted to ensure backwards compatibility
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GraphFileFormatError.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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GraphIODb.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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GraphIOGDLFile.java
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635
(12 years ago)
by duarte:
Changed default gravity value and default IDENTITY_SCORE for similarity graph
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GraphIdNotFoundError.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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IntPairComparator.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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IntPairSet.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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Interval.java
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515
(13 years ago)
by stehr:
Interval: allow spaces in residue selection strings
RIGNbhood: added method getNeighbors
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IntervalSet.java
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592
(12 years ago)
by stehr:
fixed one null pointer bug and some spelling mistakes
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MaxClusterRunner.java
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585
(12 years ago)
by stehr:
added method calculateSequenceIndependentMatrix()
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MsdsdInconsistentResidueNumbersError.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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MsdsdPdb.java
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639
(12 years ago)
by duarte:
Implemented parsing of PsiPred secondary structure prediction files in SecondaryStructure class.
New member in SecondaryStructure: sequence. Constructor must pass the sequence now, changed all references.
New method in Alignment to print a "graphical" matching of secondary structures.
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NbhProbDistribution.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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NbhoodBackgrnd.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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PairwiseAlignmentConverter.java
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517
(13 years ago)
by duarte:
Changed Alignment class so that both alignment and sequence indexing are starting at 1 (before alignment indices were starting at 0). Also mapping is now done through arrays not maps.
Changed all other classes using Alignment to accommodate this.
NOTE: graph averaging hasn't been tested after the change
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PairwiseSequenceAlignment.java
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575
(12 years ago)
by filippis:
reconstruct:
-rmsd to mirrored pdb has been added in the report file
Pdb:
-comment for outputing missing atoms added
PairwiseSequenceAlignment:
-constructor with parameters openScore and extendScore for the gaps has been added
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Pdb.java
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672
(12 years ago)
by filippis:
chechScop now looks also for chain A in scop.cla when pdbChainCode is NULL
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PdbChainCodeNotFoundError.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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PdbCodeNotFoundError.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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PdbLoadError.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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PdbaseInconsistencyError.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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PdbasePdb.java
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639
(12 years ago)
by duarte:
Implemented parsing of PsiPred secondary structure prediction files in SecondaryStructure class.
New member in SecondaryStructure: sequence. Constructor must pass the sequence now, changed all references.
New method in Alignment to print a "graphical" matching of secondary structures.
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PdbfileFormatError.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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PdbfilePdb.java
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661
(12 years ago)
by stehr:
Now enforcing that atom serials have to be in ascending order
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PirFileFormatError.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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PredEval.java
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563
(12 years ago)
by duarte:
Added new convenience method printSummary
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ProtStructGraph.java
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659
(12 years ago)
by stehr:
Also adding caspParents member to graph classes, value will be kept from Pdb if present; adding method to GraphAverager to retrieve the most frequently used parents specified in the templates
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RIGCommonNbhood.java
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512
(13 years ago)
by duarte:
Added getCommanSeparatedResSerials to RIGCommonNbhood
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RIGEdge.java
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546
(12 years ago)
by duarte:
New feature in GraphAverager: method to write the voters together with the edges; new constructor taking a RIGEnsemble
Fixed bug in RIGEnsemble: was not working for cif files.
Added a graph averaging output to main() in RIGEnsemble
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RIGEnsemble.java
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614
(12 years ago)
by stehr:
PdbfilePdb: catching previously unhandled NumberFormatException, added method setSequence() to override sequence read from file (needed for Casp prediction where 'real' sequence is known but residues may be missing in prediction)
RIGEnsemble: many changes
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RIGNbhood.java
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529
(12 years ago)
by spriya:
Drop sequence comparison in compare. Now we compare only length
New method getSize in RIGNbhood to be used instead of size that returns neighborhood size + 1
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RIGNode.java
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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RIGraph.java
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644
(12 years ago)
by duarte:
New feature: averageGraph now also writes out the CASP RR file (if -c specified) for the average graph at Cb 8.
Made a bit prettier the CASP RR output: now contacts sorted and weights with only 2 decimal figures.
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Scop.java
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589
(12 years ago)
by duarte:
New classes Template, TemplateList to be used in homology modelling pipeline.
Modified BlastUtils to use TemplateList class
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ScopRegion.java
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589
(12 years ago)
by duarte:
New classes Template, TemplateList to be used in homology modelling pipeline.
Modified BlastUtils to use TemplateList class
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SecStrucElement.java
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639
(12 years ago)
by duarte:
Implemented parsing of PsiPred secondary structure prediction files in SecondaryStructure class.
New member in SecondaryStructure: sequence. Constructor must pass the sequence now, changed all references.
New method in Alignment to print a "graphical" matching of secondary structures.
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SecondaryStructure.java
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639
(12 years ago)
by duarte:
Implemented parsing of PsiPred secondary structure prediction files in SecondaryStructure class.
New member in SecondaryStructure: sequence. Constructor must pass the sequence now, changed all references.
New method in Alignment to print a "graphical" matching of secondary structures.
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Template.java
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651
(12 years ago)
by duarte:
New class PhiPsiAverager to get consensus of phi/psi angles from a TemplateList and an Alignment. Tested with a few examples and seems to work. The wrapping of angles at 180/-180 is not yet taking into account, i.e. if an interval falls in the region just below 180 and just above -180, no consensus will be found.
Pdb: added some checks to methods getPhi/Psi so that it doesn't fail when there's no coordinates.
Changed yet again the design of TemplateList/Template. Now loading of PDB data happens upon call of the loadPDBdata method. Changed dependencies accordingly.
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TemplateList.java
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651
(12 years ago)
by duarte:
New class PhiPsiAverager to get consensus of phi/psi angles from a TemplateList and an Alignment. Tested with a few examples and seems to work. The wrapping of angles at 180/-180 is not yet taking into account, i.e. if an interval falls in the region just below 180 and just above -180, no consensus will be found.
Pdb: added some checks to methods getPhi/Psi so that it doesn't fail when there's no coordinates.
Changed yet again the design of TemplateList/Template. Now loading of PDB data happens upon call of the loadPDBdata method. Changed dependencies accordingly.
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aapairsBounds.dat
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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contactTypes.dat
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492
(13 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
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